Foot-and-mouth disease (FMD) is a highly contagious disease of livestock affecting animal production and trade throughout Asia and Africa. Understanding FMD virus (FMDV) global movements and evolution can help to reconstruct the disease spread between endemic regions and predict the risks of incursion into FMD-free countries. Global expansion of a single FMDV lineage is rare but can result in severe economic consequences. Using extensive sequence data we have reconstructed the global space-time transmission history of the O/ME-SA/Ind-2001 lineage (which normally circulates in the Indian sub-continent) providing evidence of at least 15 independent escapes during 2013–2017 that have led to outbreaks in North Africa, the Middle East, Southeast Asia, the Far East and the FMD-free islands of Mauritius. We demonstrated that sequence heterogeneity of this emerging FMDV lineage is accommodated within two co-evolving divergent sublineages and that recombination by exchange of capsid-coding sequences can impact upon the reconstructed evolutionary histories. Thus, we recommend that only sequences encoding the outer capsid proteins should be used for broad-scale phylogeographical reconstruction. These data emphasise the importance of the Indian subcontinent as a source of FMDV that can spread across large distances and illustrates the impact of FMDV genome recombination on FMDV molecular epidemiology.

Prompt confirmation and diagnosis of disease are key factors in controlling outbreaks. The development of sampling techniques to detect FMDV RNA from the environment will extend the tool kit available for the surveillance of this pathogen. The methods presented in this article broaden surveillance opportunities using accessible techniques. Pairing these methods with existing and novel diagnostic tests will improve the capability for rapid detection of outbreaks and implementation of timely interventions to control outbreaks. In areas of endemicity, these methods can be implemented to extend surveillance beyond the investigation of clinical cases, providing additional data for the assessment of virus circulation in specific areas.

Livestock markets are considered vital parts of the agricultural economy, particularly in developing countries where livestock keeping contributes to both food security and economic stability. Animals from diverse sources are moved to markets, they mix while they are there and are subsequently redistributed over wide geographic areas. Consequently, markets provide an opportunity for targeted surveillance for circulating pathogens. This study investigated the use of environmental sampling at a live goat market in Nepal for the detection of foot‐and‐mouth disease virus (FMDV) and peste des petits ruminants virus (PPRV), both of which are endemic. Five visits to the market were carried out between November 2016 and April 2018, with FMDV RNA detected on four visits and PPRV RNA detected on all five visits. Overall, 4.1% of samples (nine out of 217) were positive for FMDV RNA and 60.8% (132 out of 217) were positive for PPRV RNA, though the proportion of positive samples varied amongst visits. These results demonstrate that non‐invasive, environmental sampling methods have the potential to be used to detect circulation of high priority livestock diseases at a live animal market and, hence, to contribute to their surveillance and control.

Background: Tick-borne protozoan parasites (TBPPs) cause significant problems for domestic animals’ health in Nepal. TBPPs are routinely diagnosed by labor-intensive blood smear microscopy. In Nepal, there are some reports of Babesia and Theileria in cattle, although species identification is rarely performed. Therefore, we performed conventional nested PCR (nPCR) followed by sequence analysis to identify TBPP species infecting cattle in Nepal. Methods: One hundred and six blood samples were collected from cattle in the Kathmandu Valley. Thin blood smears were prepared for microscopic examination. Parasite DNA was extracted from the blood, and nPCR and sequencing were performed to identify the TBPPs present. Results: Among the 106 samples, 45 (42.5%) were positive for piroplasm (Babesia spp. and Theileria spp.) via microscope observation and 56 (52.8%) samples were positive via nPCR. The obtained PCR products were used for direct sequencing, and we identified the species as B. bigemina, B. bovis, T. annulate and T. orientalis. Phylogenetic analyses showed that the B. bovis, B. bigemina and T. orientalis sequences from this study belonged to each species clade. On the other hand, T. annulate was divided into two clades in the analysis, and our T. annulate sequences were also divided in these two clades. The piroplasm-positive cattle showed lower hemoglobin and red blood cells than healthy cattle. Conclusions: To the best of our knowledge, this study is the first to apply molecular detection and species determination of TBPPs in cattle in Nepal. The results of this study may be used as a starting point for the development of successful TBPP surveillance and prevention programs in Nepal.

Foot and mouth disease (FMD) is endemic in Nepal and significantly impacts the livelihood of farmers, national economy, and trade of Nepal. However, outbreak investigations are not frequently conducted, and there have been limited studies to understand the associated risk factors. A case-control study was performed in dairy cattle farms of Shankharapur and Kageshwari Municipalities, Kathmandu from March to April 2020 to describe the outbreak and identify the risk factors associated with FMD. There were 31 case farms, while 62 farms were selected as control farms (1:2). The information from case and control farms was collected by semi-structured questionnaire survey through field visits and observations. The univariable and multivariable logistic regressions were performed. The farm-level prevalence of FMD was 25.2% (n=31/123). Among the FMD affected farms, the proportion of positive farms in Shankharapur (61.3% (19/31)) was significantly higher than Kageshwori (38.7% (12/31)). The final multivariable logistic regression analysis identified four variables: cattle purchased within 14 days (OR=12.9; CI=2.4-69.5), milk market distance less than two kilometers from the farm (OR=32.7; CI=5.8-186.3), sharing of the bull from other farms for natural insemination (OR=5.7; CI=1.2-26.8), and no vaccination against FMD in the past six months (OR=19.1; CI=2.0-186.2) as significant risk factors for the occurrence of FMD. This study suggests farmers vaccinate their dairy cattle with FMD vaccine as per the vaccination schedule suggested by the veterinarians, practice quarantine measures when new animals are introduced to their farms, practice biosecurity measures in their farms, and do not use bulls from areas where there are ongoing FMD outbreaks.